Comments (2)
Hi Yuhan,
May I know if there is any specific error of using sample_for_pdb.py
for sampling? You could just use the pdb file of the specific protein pocket for this script.
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Hi Dr. Huang,
Thank you for the reply, I will test this method according to your suggestions
Another question is I noticed that the loss is around 700 after 500 epoch based on the whole crossdocked dataset, and I found the reason for this large loss value is mainly due to the loss_pos (especially contribute by loss_pos_local), I don't know if you've noticed this in your previous training or do you think this loss is normal?
I am looking forward your reply.
Best,
Yuhan
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Related Issues (20)
- Training loss does not decrease
- Training loss does not decrease HOT 6
- sample_frag.py doesn't keep the seed frag fixed HOT 9
- Code Issue HOT 1
- Inquiry on Utilizing Your Trained Model for Molecule Generation in Protein Pockets HOT 7
- No matching distribution found for mkl==2017.0.3 HOT 1
- Unexpected Results in Sampling for Custom Pockets HOT 4
- sample_for_pdb.py error HOT 3
- sample_linker doesn't add atoms totally in the broken site HOT 1
- How to generate .lmdb and .pt file before training? HOT 1
- How to generate bond HOT 2
- mat1 and mat2 shapes cannot be multiplied (389x10 and 8x128) HOT 2
- Read ligand sdf file error
- There is no evaluate.py function HOT 1
- There is no prepare_receptor4.py in the evaluation/ directory HOT 1
- Description of cut pocket process HOT 3
- miss data/2VUKcut10/2VUKcut10_pocket.pdb
- installing question HOT 16
- cannot get date in Data preparation
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